Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine

From: Pallavi Mohanty <>
Date: Fri, 4 Dec 2015 14:57:35 +0530

Thanks Dac for your inputs! Actually I did tried tleap first but because
of bad atom typing of some residues was not able to generate the necessary
parameter files. Then I tried my hands on antechamber but it was again a
failure as I was giving the entire complex as an input. When i got your
response I tried running tleap again, fixed all the bad atom typing, loaded
all the libraries. And yes it worked. Thanks a lot!

On Thu, Dec 3, 2015 at 7:03 PM, David A Case <> wrote:

> On Thu, Dec 03, 2015, Pallavi Mohanty wrote:
> > I have a docked complex with one the tyrosines is phosphorylated. The
> > phosphorylated tyrosine is interacting with some residues present in the
> > other chain of the complex. I have performed the docking in HADDOCK. Now
> I
> > want to simulate the complex and I am clueless what can be the possible
> > strategy. As in i am unable to generate the topology and coordinate files
> > for the complex. Moreover I thought antechamber would be the possible
> > answer but unfortunately it says MAXATOM limit exceeds the given input.
> Amber provides standard libraries for common phosphorylated amino acids:
> use
> the leaprc.phosaa10 file as well as leaprc.ff14SB. See Section 3.2 of the
> 2015 Amber Reference Manual. Note: because the PDB standard does not
> distinguish between protonated and deprotonated phosphates, some Amber
> residue
> names are non-standard, and you will have to edit your PDB file so that the
> Amber library names are used. See the comments at the top of the
> leaprc.phosaa10 file.
> Based on very limited information, the error in antechamber may have arisen
> because you gave it an entire protein or complex file. Antechamber is
> intended for *single residues or small molecules* only.
> ...good luck...dac
> _______________________________________________
> AMBER mailing list

Pallavi Mohanty
AMBER mailing list
Received on Fri Dec 04 2015 - 01:30:05 PST
Custom Search